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Journals, Chapters and international conferences with published proceedings.

A primer on correlation-based dimension reduction methods for multi-omics analysis
Tim Downing and Nicos Angelopoulos
Journal of the Royal Society Interface, on-line 11 Oct 2023.
[10.1098/rsif.2023.0344|bib]

Transcriptome analysis reveals tumor microenvironment changes in glioblastoma
Youri Hoogstrate et al.
Cancer Cell, 41(4), 678-692, April 2023. [S1535610823000478|bib]

Bayesian networks elucidate complex genomic landscapes in cancer
Nicos Angelopoulos, Aikaterini Chatzipli, Jyoti Nangalia, Francesco Maura and Peter J. Campbell
Communications Biology 5, article 306, April 2022.
[10.1038/s42003-022-03243-w|bib]

mSep - Investigating physiological and immune-metabolic biomarkers in septic and healthy pregnant woman to predict feto-maternal immune health: A prospective observational cohort study protocol
Simran Sharma, Summia Zaher, Patricia R. S. Rodrigues, Luke C. Davies, Sarah Edkins, Angela Strang, Mallinath Chakraborty, John W. Watkins, Robert Andrews, Edward Parkinson, Nicos Angelopoulos, Linda Moet, Freya Shepherd, Kate Davies, Daniel White, Shaun Oram, Kate Siddall, Vikki Keeping, Kathryn Simpson, Federica Faggian, Maryanne Bray, Claire Bertorelli, Sarah Bell, Rachel Collis, James E. McLaren, Mario Labeta, Valerie B. O'Donnell, and Peter Ghazal
BMJ Open, 12(9), September 2022.
[Journal: e066382|bib]

mmsig: a fitting approach to accurately identify somatic mutational signatures in hematological malignancies
Even H. Rustad, Ferran Nadeu, Nicos Angelopoulos, Bachisio Ziccheddu, Niccolo Bolli, Xose S. Puente, Elias Campo, Ola Landgren and Francesco Maura
Communications Biology 4, article 424, March 2021.
[s42003-021-01938-0|bib|Cardiff]

Revealing the impact of structural variants in multiple myeloma
E. H. Rustad, V. D. Yellapantula, D. Glodzik, K. H. Maclachlan, B. Diamond, E. M. Boyle, C. Ashby, P. Blaney, G. Gundem, M. Hultcrantz, D. Leongamornlert, N. Angelopoulos, L. Agnelli, D. Auclair, Y. Zhang, A. Dogan, N. Bolli, E. Papaemmanuil, K. C. Anderson, P. Moreau, H. Avet-Loiseau, N. C. Munshi, J. J. Keats, P. J. Campbell, G. J. Morgan, O. Landgren and F. Maura
Blood Cancer Discovery, 2020 (on-line 15th Sept. 2020)
[10.1158/2643-3230.BCD-20-0132 | bib]

Timing the initiation of multiple myeloma
E. H. Rustad, V. Yellapantula, D. Leongamornlert, N. Bolli, G. Ledergor, F. Nadeu, N. Angelopoulos, K. J. Dawson, T. J. Mitchell, R. J. Osborne, B. Ziccheddu, C. Carniti, V. Montefusco, P. Corradini, K. C. Anderson, P. Moreau, E. Papaemmanuil, L. B. Alexandrov, X. S. Puente, E. Campo, R. Siebert, H. Avet-Loiseau, O. Landgren, N. Munshi, P. J. Campbell and F. Maura
Nature Communications volume 11, Article number: 1917 (2020). 21st April 2020.
[10.1038/s41467-020-15740-9 | bib]

Targeting of EGFR by a combination of antibodies mediates unconventional EGFR trafficking and degradation
S. Jones, P. J. King, C. N. Antonescu, M. G. Sugiyama, A. Bhamra, S. Surinova, N. Angelopoulos, M. Kragh, M. W. Pedersen, J. A. Hartley and C. E. Futter
Scientific Reports volume 10, Article number: 663 (2020).
[10.1038/s41598-019-57153-9 | bib]

Molecular Evolution of IDH Wild-Type Glioblastomas Treated With Standard of Care Affects Survival and Design of Precision Medicine Trials: A Report From the EORTC 1542 Study
K. Draaisma, A. Chatzipli, M. Taphoorn, M. Kerkhof, A. Weyerbrock, M. Sanson, A. Hoeben, S. Lukacova, G. Lombardi, M. Hanse, R. Fleischeuer, S. Leenstra, C. Watts, J. McAbee, N. Angelopoulos, T. Gorlia, V. Golfinopoulos, J. M. Kros, R.G.W. Verhaak, M.J. van den Bent, U. McDermott, P. A. Robe and P. J. French
Journal of Clinical Oncology, 38 (1), (January 01, 2020) 81-99.
[10.1200/JCO.19.00367 | bib]

Genomic Landscape and Chronological Reconstruction of Driver Events in Multiple Myeloma
Francesco Maura, Niccolo Bolli, Nicos Angelopoulos, Kevin J. Dawson, Daniel Leongamornlert, Inigo Martincorena, Federico Abascal, Thomas J. Mitchell, Anthony Fullam, Santiago Gonzalez, Raphael Szalat, Bernardo Rodriguez-Martin, Mehmet Kemal Samur, Dominik Glodzik, Marco Roncador, Mariateresa Fulciniti, Yu Tzu Tai, Stephane Minvielle, Florence Magrangeas, Philippe Moreau, Paolo Corradini, Kenneth Anderson, Jose M. C. Tubio, David C. Wedge, Moritz Gerstung, Herve Avet-Loiseau, Nikhil Munshi and Peter J. Campbell
Nature Communications 10, Article number: 3835 (2019).
[10.1038/s41467-019-11680-1 | bib]

Advances in big data bio analytics
Nicos Angelopoulos and Jan Wielemaker
In International Conference on Logic Programming, ICLP 2019 (as Technical Communication), September 2019.
[1909.08254 | 10.4204/EPTCS.306.36 | 1909.08254 | bib]

Classification and Personalized Prognosis in Myeloproliferative Neoplasms
Jacob Grinfeld, Jyoti Nangalia, E. Joanna Baxter, David C. Wedge, Nicos Angelopoulos, Robert Cantrill ... Peter J. Campbell
New England Journal of Medicine, 379:1416-1430, October 11, 2018.
[10.1056/NEJMoa1716614 | NEJMoa1716614 | Cambridge Uni: 283087 | bib]

Timing the landmark events in the evolution of clear cell renal cell cancer.
Thomas J. Mitchell, Samra Turajlic, Andrew Rowan, David Nicol, James HR Farmery, Tim O'Brien, Inigo Martincorena, Patrick Tarpey, Nicos Angelopoulos, ..., Charles Swanton and Peter J Campbell
Cell, 173(3):611-623, April 2018.
[10.1016/j.cell.2018.02.020 | cell30164-8 | bib]

Biological and prognostic impact of APOBEC-induced mutations in the spectrum of plasma cell dyscrasias and multiple myeloma cell lines
Francesco Maura et al.
Leukemia, 2017.
[10.1038/leu.2017.345
| leu2017345 | bib]

Accessing biological data as Prolog facts
Nicos Angelopoulos and Jan Wielemaker
In the 19th International Symposium on Principles and Practice of Declarative Programming (PPDP 2017)
9-11 October, 2017. Namur, Belgium.
[10.1145/3131851.3131857
| ppdp_2017 | pdf: acm.pdf | bib]

Distributional Logic Programming for Bayesian Knowledge Representation
Nicos Angelopoulos and James Cussens
International Journal of Approximate Reasoning (IJAR)
Volume 80, January 2017, pages 52-66.
[j.ijar.2016.08.004 | preprint: Bims | bib]

Advances in integrative statistics for logic programming
Nicos Angelopoulos, Samer Abdallah and Georgios Giamas
International Journal of Approximate Reasoning, (IJAR)
Volume 78, November 2016, pages 103-115.
[j.ijar.2016.06.008 | preprint: Real | bib]

Proteome-wide dataset supporting functional study of tyrosine kinases in breast cancer
Nicos Angelopoulos, Justin Stebbing, Yichen Xu, Georgios Giamas and Hua Zhang
Data-in-Brief (DiB), Volume 7, 740-746, June 2016
[10.1016/j.dib.2016.03.024 | bib]

ATG9A loss confers resistance to trastuzumab via c-Cbl mediated Her2 degradation
Joao Nunes, Hua Zhang, Nicos Angelopoulos, Jyoti Chetri, Clodia Osipo, Justin Stebbing and Georgios Giamas
Oncotarget, Vol 7, No 19, 27599-27612, March 2016
[10.18632/oncotarget.8504 | bib]

Proteomic profile of KSR1-regulated signalling in response to genotoxic agents in breast cancer
Hua Zhang, Nicos Angelopoulos, Yichen Xu, Arnhild Grothey, Joao Nunes, Justin Stebbing and Georgios Giamas
Breast Cancer Research and Treatment (BCRT), 151(3):555-568, June 2015.
Joint first author.
[10.1007/s10549-015-3443-y | bib]

Characterization of the Tyrosine Kinase-Regulated Proteome in Breast Cancer by Combined use of RNA interference (RNAi) and Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) Quantitative Proteomics.
Justin Stebbing, Hua Zhang, Yichen Xu, Arnhild Grothey, Joao Nunes, Nicos Angelopoulos and Georgios Giamas
Molecular and Cellular Proteomics (MCP), 14(9):2479-92, September 2015.
Joint last author.
[10.1074/mcp.M115.048090 | bib]

LMTK3 represses tumor suppressor-like genes through chromatin remodeling in breast cancer
Yichen Xu, Hua Zhang, Van T Thuy Mai Ngyuen, Nicos Angelopoulos, Joao Nunes, Alistair Reid, Laki Buluwela, Luca Magnani, Justin Stebbing and Georgios Giamas
Cell Reports, 12(5), 837-849, August 2015.
[10.1016/j.celrep.2015.06.073 | bib]

A logical approach to working with biological databases
Nicos Angelopoulos and Georgios Giamas
Proceedings of the 31st International Conference on Logic Programming.
ICLP '15, (technical communication), Cork, September 2015.
[tc_74 | bib]

The vaginal microbiome during pregnancy and the postpartum period in a European population
David MacIntyre, Manju Chandiramani, Yun S Lee, Lindsay Kindinger, Ann Smith, Nicos Angelopoulos, Benjamin C. Lehne, Shankari Arulkumaran, Richard Brown, Tiong Ghee Teoh, Elaine Holmes, Jeremy K. Nicholson, Julian Marchesi and Phillip R. Bennett
Scientific Reports, 5(article 8988), 2015.
[10.1038/srep08988 | bib]

Quantitative imaging of focal adhesion dynamics and their regulation by HGF and Rap1 signaling
Emma Spanjaard, Ihor Smal, Nicos Angelopoulos, Ingrid Verlaan, Alexandre Matov, Erik Meijering, Lodewyk Wessels, Hans Bos and Johan de Rooij
Experimental Cell Research (ECR), 330(2), 382-397, 2015.
[10.1016/j.yexcr.2014.10.012 | bib]

Integrative functional statistics in logic programming
Nicos Angelopoulos, Vitor Santos Costa, Joao Azevedo, Jan Wielemaker, Rui Camacho and Lodewyk Wessels
Proc. of Practical Aspects of Declarative Languages (PADL 2013).
LNCS vol. 7752, p. 190-205 .January, 2013. Rome, Italy).
[10.1007/978-3-642-45284-0_13 | padl2013-real.pdf | bib]

ProSQLite: Prolog file based databases via an SQLite interface
Canisius Sander, Nicos Angelopoulos and Lodewyk Wessels
Proc. of Practical Aspects of Declarative Languages (PADL 2013).
LNCS vol. 7752, p. 222-227 .January, 2013. Rome, Italy).
[10.1007/978-3-642-45284-0_15 | padl2013-prosqlite.pdf | bib]
Joint first author.

Learning binding affinity from augmented high throuput screening data.
Nicos Angelopoulos, Andreas Hadjiprocopis and Malcolm D. Walkinshaw
Chapter in "Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques", (book), IGI Book Series on Chemoinformatics.
Huma Lodhi and Yoshihiro Yamanishi (Eds).
Chapter 11, 312-324, 2010.
[10.4018/978-1-61520-911-8.ch011 | bib]

Selective Chemical Intervention in the Proteome of Caenorhabditis elegans
Hoger Husi, Fiona McAllister, Nicos Angelopoulos, Victoria J. Butler, Kevin R. Bailey, Kirk Malone, Logan MacKay, Paul Taylor, Antony P. Page, Nicholas J. Turner, Perdita E. Barran, and Malcolm Walkinshaw
Journal of Proteome Research, (JPR), 9(11), 6060-6070, 2010.
[10.1021/pr100427c | bib ]

Bayesian ligand discovery from high dimensional descriptor data
Nicos Angelopoulos, Andreas Hadjiprocopis and Malcolm D. Walkinshaw.
ACS Journal of Chemical Information and Modeling, (JCIM), 49(6), 1547-1557, 2009.
[10.1021/ci900046u]

Bayesian learning of Bayesian Networks with informative priors.
Nicos Angelopoulos and James Cussens (2008).
Special issue on BN learning. Annals of Mathematics and Artificial Intelligence (AMAI) 54(1-3), 53-98.
[10.1007/s10472-009-9133-x | amai.pdf | bib]

Exploiting Informative Priors for Bayesian Classification and Regression Trees.
Nicos Angelopoulos and James Cussens (2005)
In 19th International Joint Conference on Artificial Intelligence (IJCAI-05), 641-646, Edinburgh, UK, August 2005.
[dl.acm.org | ijcai05.pdf | bib]

Tempering for Bayesian C\&RT.
Nicos Angelopoulos and James Cussens.
In 22nd International Conference on Machine Learning (ICML 2005), 17-24, Bonn, Germany, August 2005.
[10.1145/1102351.1102354 | icml05.pdf | bib]

Probabilistic space partitioning in Constraint Logic Programming.
Nicos Angelopoulos.
In 9th Asian Computing Science Conference, (LNCS 3321) 48-62, Chiang Mai, Thailand, December 2004.
[10.1007/978-3-540-30502-6_4 | Asian04.ps.gz | bib]

Prolog Issues and Experimental Results of an MCMC Algorithm.
Nicos Angelopoulos and James Cussens.
In Web-Knowledge Management and Decision Support -
Selected Papers from the 14th International Conference on Applications of Prolog,
191-202, LNAI (2543).
U. Geske, O. Bartenstein, M. Hannebauer and O. Yoshie (eds.). Springer, 2002.
[10.1007/3-540-36524-9_15 | Lnai2002.ps.gz | bib]

Architecture of a Mediator for a Bioinformatics Database Federation.
G.J.L. Kemp, N. Angelopoulos and P.M.D. Gray (2002)
IEEE Transactions on Information Technology in Biomedicine (TITB), 6(2):116-122.
[10.1109/TITB.2002.1006298 | bib]

Machine Learning Metabolic Pathway descriptions using a Probabilistic Relational Representation.
Nicos Angelopoulos and Stephen Muggleton.
In Electronic Transactions in Artificial Intelligence (ETAI), 7(9):1-11, 2002.
[MI19.ps.gz | bib]

Markov chain Monte Carlo using tree-based priors on model structure.
Nicos Angelopoulos and James Cussens (2001).
In 17th Conference on Uncertainty in Artificial Intelligence (UAI-2001), 16-23, Seattle, USA.
[dl.ac.org | uai01.pdf | bib]

CORBA and XML: Design Choices for Database Federations.
Graham Kemp, Chris J Robertson, Peter M. D. Gray and Nicos Angelopoulos (2000)
In Advances in Databases: Proceedings of the Seventeenth British National Conference on Databases (BNCOD 17),
Lecture Notes in Computer Science (1832), Lings, B. and Jeffery, K. (eds.), Springer-Verlag, Berlin, pp 191-208.
[10.1007/3-540-45033-5_14 | bncod17.pdf | bib]

Other conferences and workshops

Notes on the Implementation of FAM
In 3rd Workshop in Probabilistic Logic Programming (PLP'16)
September 3rd, 2016, London, UK
Nicos Angelopoulos
[1661/05]

Choline metabolism is an early predictor of EGFR-mediated survival in NSCLC
Rosy Favicchio, Nicos Angelopoulos, Diana Brickute, Robin Fortt, Frazer Twyman, Georgios Giamas, Juan Carlos Lacal and Eric O. Aboagye
In the 107th Annual Meeting of the American Association for Cancer Research,
April, 2016, New Orleans, Louisiana.
[abstracts book]

Advances in integrating statistical inference
Nicos Angelopoulos, Samer Abdallah and Georgios Giamas
2nd Workshop on Probabilistic Logic Programming (September, 2015. Cork, Ireland).
[ceur:Vol-1413/paper-01]

SILAC-based analysis reveals a unique phosphoproteomic-signature of HER2-resistant breast cancer cells
Joao Farinha Garcao Nunes, Hua Zhang, Justin Stebbing, Nicos Angelopoulos and Georgios Giamas
Anticancer Research 34(10), 5900, 2014.
[Abstracts]

Prolog bioinformatic pipelines: a case study in gene dysregulation
Nicos Angelopoulos and Georgios Giamas
Workshop on Constraint-Based methods for Bioinformatics (WCB'14), (September, 2014. Lyon, France).
[WCB_14]

Search and Rescue: logic and visualisation of biochemical networks
Nicos Angelopoulos, Paul Shannon and Lodewyk Wessels
Workshop on Constraints in Bioinformatics, p.1-6, (September, 2012. Budapest, Hungary).
[wcb2012.pdf | bib]

Syntactic integration of external languages in Prolog
Jan Wielemaker and Nicos Angelopoulos
ICLP Workshop on Logic-based methods in Programming Environments, p. 40-50, (September, 2012. Budapest, Hungary).
[wlpe2012-JW.pdf | bib]

Exploring file based databases via an Sqlite interface
Canisius Sander, Nicos Angelopoulos and Lodewyk Wessels
ICLP Workshop on Logic-based methods in Programming Environments, p.2-9, (September, 2012. Budapest, Hungary).
[wlpe2012_sqlite.pdf | bib]

Effective priors over model structures applied to DNA binding assay data
Nicos Angelopoulos and Lodewyk Wessels (2011)
AIME'11 Workshop on Probabilistic Problem Solving in Biomedicine Bled, Slovenia, July 2011.
[probbiomed.pdf | proceedings]

An extensible web interface for databases and its application to storing biochemical data
Nicos Angelopoulos and Paul Taylor.
In WLPE workshop, July 2010.
[CoRR|local:wlpe2010.pdf]

Distributional logic programs: a brief overview.
Nicos Angelopoulos.
In NIPS'08 Workshop, Probabilistic Programming: Universal Languages, Systems and Applications Whistler, CA. 2008.
[nips08_prbpro.pdf | bib ]

Exploiting independence for branch operations in Bayesian learning of C&RTs.
Nicos Angelopoulos and James Cussens.
In Probabilistic, Logical and Relational Learning - Towards a Synthesis. Dagstuhl Seminar Proceedings, Schloss Dagstuhl, Germany, Dagstuhl, Germany, 2006.
[415 | bib ]

Extended stochastic logic programs for informative priors over C\&RTs.
Nicos Angelopoulos and James Cussens.
In Proceedings of the work-in-progress track of the Fourteenth International Conference on Inductive Logic Programming (ILP04), 7-11, Porto, Portugal, September 2004.
[ilp04_wip.pdf | bib ]

Upsh: A Unix to Prolog Shell.
Nicos Angelopoulos.
In Workshop on Logic Programming Environments. Satellite workshop to ICLP'04, Saint-Malo, France, 2004.
[Wple04.ps.gz | bib ]

On the implementation of MCMC proposals over Stochastic Logic Programs.
Nicos Angelopoulos and James Cussens.
In Colloquium on Implementation of Constraint and LOgic Programming Systems. Satellite workshop to ICLP'04, Saint-Malo, France, 2004.
[Ciclops04.ps.gz | bib ]

clp(pfd(Y)): Constraints for Probabilistic Reasoning in Logic Programming.
Nicos Angelopoulos.
In 9th International Conference on Principles and Practice of Constraint Programming, 784-788, Kinsale, Ireland, October 2003.
[nicos_cp03.ps.gz | bib ]

Nicos Angelopoulos.
Extending the CLP engine for Reasoning under Uncertainty.
In 14th International Symposium on Methodologies for Intelligent Systems, 365-373, Maebashi, Japan, October 2003.
[Ismis03.ps.gz | bib ]

Exporting Prolog source code.
Nicos Angelopoulos.
In Workshop on Logic Programming Environments. Satellite workshop to ICLP'02, 89-96, Copenhagen, Denmark, 2002.
[02-Wlpe.pdf | bib ]

Prolog issues of an MCMC algorithm.
Nicos Angelopoulos and James Cussens.
In Proceedings of the 14th International Conference of Applications of Prolog INAP2001, 246-253, Tokyo, Japan, October 2001.
[10.1007/3-540-36524-9_15 | Inap01.ps.gz | bib ]

A Statistical View of Probabilistic Finite Domains.
Nicos Angelopoulos and David R. Gilbert.
In Workshop on Quantitative Aspects of Programming Laguages (QAPL'01), Satellite to Principles, Logics, and Implementations of high-level programming languages, (PLI'01), Firenze, Italy, 2001.
[Qapl01.ps.gz | bib ]

A Schema-based Approach to Building a Bioinformatics Database Federation.
Graham Kemp, Nicos Angelopoulos and Peter M. D. Gray.
In IEEE International Symposium on Bio-Informatics and Biomedical Engineering, 13-20, Washington, USA, 2000.
[Bibe2000.ps.gz | bib ]

Theses, Technical Reports and Posters

Timing the initiation of multiple myeloma
Francesco Maura, Even Rustad, Venkata Yellapantula, Niccolo Bolli, Daniel Leongamornlert, Ferran Nadeu, Nicos Angelopoulos, Kevin Dawson, Thomas Mitchell, Rob Osborne, Bachisio Ziccheddu Ziccheddu, Cristiana Carniti, Vittorio Montefusco, Paolo Corradini, Kenneth C. Anderson, Philippe Moreau, Elli Papaemmanuil, Ludmil Alexandrov, Xose Puente, Elias Campo, Reiner Siebert, Herve Avet-Loiseau, Nikhil Munshi, Peter Campbell, C. Ola Landgren
In 17 International Myeloma Workshop, 12-15 September, 2019. Boston, MA, USA.
Proceedings from IMW website: 17th_IMW_Abstract_Book_FINAL_V2.pdf ]

Markov chain Monte Carlo over Model Structures
Nicos Angelopoulos and James Cussens
In ALP Newsletter, focus on Probabilistic Prolog Systems, June 2011.
[alp2011_mcmcms.pdf, ALP website: pepl.pdf ]

PEPL: An implementation of FAM for SLPs
Jianzhong Chen, Stephen Muggleton, James Cussens and Nicos Angelopoulos In ALP Newsletter, focus on Probabilistic Prolog Systems, June 2011.
[alp2011_pepl.pdf , ALP website: pepl.pdf ]

SLPs for Probabilistic Pathways: Modelling and Parameter Estimation.
Nicos Angelopoulos and Stephen Muggleton.
Technical Report 2002/12. Department of Computing, Imperial College, London, UK, 2002.
[DTR02-12.pdf | bib ]

Probabilistic Finite Domains: A Brief Overview.
Nicos Angelopoulos.
In International Conference on Logic Programming, 475, Copenhagen, Denmark, 2002.
[Iclp02.ps.gz | bib ]

Probabilistic Finite Domains.
Nicos Angelopoulos.
PhD Thesis, Department of Computing Science, City University, London, UK. 2001.
[Thesis_Abstract.html | bib ]

Implementing Randomised Algorithms in Constraint Logic Programming.
N. Angelopoulos, A. Di Pierro and H. Wiklicky.
In Joint International Conference and Symposium on Logic Programming, JICSLP'98, 355-356, Manchester, UK, 1998.
[Jicslp98.ps.gz | bib ]

Randomised Algorithms and Constraint Logic Programming.
Nicos Angelopoulos, Alessandra Di Pierro and Herbert Wiklicky.
Technical Report TR-1998-02. City University, London, UK, March 1998.
[TR98-02.ps.gz | bib ]

Constraint-Logic Based Approach to Scheduling.
Nicos Angelopoulos.
Masters Thesis, Department of Computing, Imperial College, London, UK, 1993.
[MScThesis.ps.gz | bib ]


Nicos Angelopoulos, 2023-10-11